The mitogenome of Phytophthora agathidicida: Evidence for a not so recent arrival of the “kauri killing” Phytophthora in New Zealand

Abstract

Phytophthora agathidicida is associated with a root rot that threatens the long-term survival of the iconic New Zealand kauri. Although it is widely assumed that this pathogen arrived in New Zealand post-1945, this hypothesis has yet to be formally tested. Here we describe evolutionary analyses aimed at evaluating this and two alternative hypotheses. As a basis for our analyses, we assembled complete mitochondrial genome sequences from 16 accessions representing the geographic range of P. agathidicida as well as those of five other members of Phytophthora clade 5. All 21 mitogenome sequences were very similar, differing little in size with all sharing the same gene content and arrangement. We first examined the temporal origins of genetic diversity using a pair of calibration schemes. Both resulted in similar age estimates; specifically, a mean age of 303.0–304.4 years and 95% HPDs of 206.9–414.6 years for the most recent common ancestor of the included isolates. We then used phylogenetic tree building and network analyses to investigate the geographic distribution of the genetic diversity. Four geographically distinct genetic groups were recognised within P. agathidicida. Taken together the inferred age and geographic distribution of the sampled mitogenome diversity suggests that this pathogen diversified following arrival in New Zealand several hundred to several thousand years ago. This conclusion is consistent with the emergence of kauri dieback disease being a consequence of recent changes in the relationship between the pathogen, host, and environment rather than a post-1945 introduction of the causal pathogen into New Zealand.

Comparative Analyses of Complete Peronosporaceae (Oomycota) Mitogenome Sequences—Insights into Structural Evolution and Phylogeny

“…Mitogenome sequences might also be used to estimate the timeframe over which Peronosporaceae have evolved. Matari and Blair (2013) used a multilocus nuclear data set to estimate divergence times for the oomycetes and complete mitogenome sequences have been used for age estimation in Phytophthora (e.g., Martin et al 2016 ; Winkworth et al 2021 ). Matrices of mitogenome sequences are relatively long and this is encouraging in terms of resolving the timeframe over which the Peronosporaceae have evolved.…”

Kauri Dieback Prevention: Relational Values of Knowledge Producers

“…Hence it is posited that the disease risk is not an accurate reflection of the pathogen risk of PA (Winkworth, 2021). That is to say, that the risk of kauri dieback symptoms being expressed may be fewer than the risk that PA is present at a location (Winkworth, 2021).…”

“…Hence it is posited that the disease risk is not an accurate reflection of the pathogen risk of PA (Winkworth, 2021). That is to say, that the risk of kauri dieback symptoms being expressed may be fewer than the risk that PA is present at a location (Winkworth, 2021). For this reason, it is difficult to determine how 'wide-spread' PA really is when the only means of visual detection are once kauri trees show symptoms.…”

“…However historical records from the early 1900s report trunk diameters upwards of 7m (Steward & Beveridge, 2010). The large stem sizes as well as good quality timber, resulted in kauri trees being subjected to relentless commercial felling and logging following European settlement (Winkworth, 2021). Today, it is estimated that less than 10% of pre-European kauri remain (Winkworth, 2021).…”

“…Other studies claimed that although PA is exotic, it was likely introduced earlier than mid-20 th Century (Froud, 2020) and had been undetected (Hood, 2021). Other scholars theorise that PA has always been in NZ soil but in a benign state, and that human activity as well as climate induced changes to the environment, have given the pathogen favourable conditions to become active (Winkworth, 2021). Hood (2021) states that "it is not uncommon for infection by native pathogens to bring about disease when the balance with their host is upset by human intervention."…”